ABSTRACT Breast cancer is a pathologically and genetically heterogeneous disease, reflecting diverse signaling pathways responsible for cancer progression. In vitro models of breast cancer must integrate the complex nature of the disease with culturing methods that closely mimic different clinical types of cancer seen in patients. In 2007, there were more than 178,000 new cases and 40,000 deaths from breast cancer, making it the second leading cause of cancer related death in women and these statistics suggest the need for the development of more effective treatments (American Cancer Society; http://www.cancer.org). Over the past ten years, most advances in chemotherapeutic treatment of breast cancer have involved the optimization of doses and scheduling of standard therapeutics. Several new targeted therapies and biologics have been approved for the treatment of breast cancer; however, many cancers do not respond to or recur even with the ideal drug regimens. Because specific molecular signatures can classify breast cancer into multiple subtypes with distinct clinical characteristics, we can now pursue the development of therapeutics with selectiveness against each individual tumor type. Thus, breast cancer must be considered a multifaceted disease with each subtype offering unique opportunities for chemotherapeutic intervention. We have developed a novel anti-cancer drug discovery screen that encompasses the cellular and genetic diversity of breast cancer. This screen is unique in that it uses murine primary tumor organoids molecularly classified as similar to actual breast cancer subtypes observed in patients. The subtype-specific tumor organoids are screened against a chemical library to identify novel small-molecule anti-cancer compounds. In parallel, the compounds are also screened for their effect on normal primary organoids. Using this screen, we identified a novel small molecule, C-6, that kills primary tumor tissue derived from both mice and humans, and subsequent structure activity relationship analyses revealed the basic pharmacophore of the molecule. Importantly, C-6 exhibits selective cytotoxicity against both basal-like and luminal cancer organoids isolated from mice and human patients, but not organoids isolated from normal mice and human tissue. This compound is structurally novel and may kill tumor cells through a unique mechanism of action. We observed that C-6 delays epithelial cell apoptosis within the lumens of normal mammary organoids; however, it did not affect branching morphogenesis of mammary organoids. The selective cytotoxicity of C-6 combined with its minimal affect on normal biological processes suggests that this compound targets a molecular pathway vital to the homeostasis of breast cancer cells. Thus, the objectives outlined in this proposal will establish the optimal pharmacophore structure of C-6, identify the molecular target(s), and evaluate its biological effects in both tumor and normal cells.